The new record was measured in the southern town of Carpentras. The previous record was 44.1 degrees Celsius during a heatwave in 2003 that killed thousands.
France's weather service issued an unprecedented red alert for four areas all in the south, but most of the country remains on orange alert, the second highest level. About 4,000 schools have been shut in France, the BBC reported.
The heatwave has already caused flash floods and forest fires, grounded planes, buckled train tracks, led to school closures and warnings over air quality in Europe.
France has set up temporary water fountains in built-up areas and is allowing public pools to open late into the night.
French Health Minister Agnès Buzyn said she was concerned about the increase in calls to emergency service numbers as a result of the heatwave. She called on members of the public to avoid "risky behaviour" like leaving children in cars or jogging outside in the middle of the day.
Swathes of the continent are experiencing sweltering heat, with Germany, Poland, the Czech Republic and others recording their highest-ever June temperatures.
In Spain, firefighters are battling Catalonia's worst wildfires in 20 years. Eight provinces are on red alert while temperatures are expected to rise above 42 degrees Celsius in many areas.
The Italian Health Ministry reported emergency levels of heat in 16 cities, the BBC said.
Two people are believed to have died from suspected heatstroke in Spain. A 17-year-old farm worker in Córdoba, went into convulsions after cooling down in the farm swimming pool, while an 80-year-old man died on a street in Valladolid city.
In the UK, the police warned people of the dangers of cooling off in rivers and lakes after a 12-year-old girl drowned in the River Irwell in Greater Manchester.
Meteorologists blame hot air drawn in from northern Africa for the extreme heat, caused by high pressure over central Europe and a storm stalling over the Atlantic.
( With inputs from IANS )